Changes between Version 2 and Version 3 of Data_exchange

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Timestamp:
2010/02/12 16:54:42 (14 years ago)
Author:
richard
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  • Data_exchange

    v2 v3  
    1919 
    2020'''Discussion on possibilities/need for improving data exchange between 
    21 e.g. InterMine, Galaxy, BioMart, Cytoscape...''' 
     21e.g. !InterMine, Galaxy, !BioMart, Cytoscape...''' 
    2222 
    2323Would typing of arbitrary data exchange improve communication between 
    … …  
    4141   needed> 
    4242 
    43    Cytoscape (http://www.cytoscape.org) & BioMart: REST API used.  Perhaps SOAP would be better but 
     43   Cytoscape (http://www.cytoscape.org) & !BioMart: REST API used.  Perhaps SOAP would be better but 
    4444   this still requires some development.  REST was fine for data 
    4545   retrieval. 
    4646 
    47    BioMart: the Mart deployer decides on the meta-data layer in 
     47   !BioMart: the Mart deployer decides on the meta-data layer in 
    4848   biomart - the GUI uses this layer rather than the data.  It assumes 
    4949   that the user understands what you are talking about.  Sometimes 
    … …  
    5454 
    5555    Interoperation of Marts: this is the only place where must get the 
    56      semantics correct.  If one mart calls something a UniProt 
     56     semantics correct.  If one mart calls something a !UniProt 
    5757     identifier and the other one does too then essential that they are 
    5858     refering to the same identifier.  Perhaps would be good to have 
    … …  
    6060     have matching values. 
    6161 
    62    InterMine (http://www.intermine.org): multiple organisms can use the same identifiers 
    63    e.g. across 12 drosophila genomes.  InterMines can ask each other 
     62   !InterMine (http://www.intermine.org): multiple organisms can use the same identifiers 
     63   e.g. across 12 drosophila genomes.  !InterMines can ask each other 
    6464   what data they provide but can't be sure name-spaces are 
    65    compatible.  Would be nice if InterMine or BioMart systems can talk 
     65   compatible.  Would be nice if !InterMine or !BioMart systems can talk 
    6666   and discover what they have and how they could communicate.  Agreed 
    6767   that would be good to have more formal description so that intended 
    68    InterMine talking to BioMart backend could be easier. 
     68   !InterMine talking to !BioMart backend could be easier. 
    6969 
    7070 
    … …  
    104104File formats vs labelling of data itself: 
    105105 
    106 BioMart/ InterMine can both provide column meaning "GO identifier", 
     106!BioMart/ !InterMine can both provide column meaning "GO identifier", 
    107107but where to assert they are the same thing? 
    108108 
    … …  
    110110 
    111111Is there a need for a central naming authority/ namespace provider? 
    112 Given work on UniProt already, is EBI an natural location for this? 
     112Given work on !UniProt already, is EBI an natural location for this? 
    113113DDBJ/ DBCLS/ NCBI? 
    114114 
    … …  
    157157  arbitrary human-friendly names are also good. 
    158158 
    159  * Agreed to dump all BioMart/ InterMine column headings out, find 
     159 * Agreed to dump all !BioMart/ !InterMine column headings out, find 
    160160    the common/commonly-used ones and work on naming. 
    161161 
    … …  
    167167the same versions of genomes.  Agreed Versioning is important. 
    168168 
    169   BioMart/ UCSC do have versions 
     169  !BioMart/ UCSC do have versions 
    170170  available but not necessarily using the same namespaces. 
    171171